The analysis of proteins and protein complexes in an effort to understand functions of proteins in a biological organism is complex and unwieldy. Some efforts have been made to separate protein complexes using one or two-dimensional separation methods, such as gel electrophoresis methods. Complexes of proteins are moved through the gel or other separation medium as intact entities (either as native interacting complexes, or covalently bound using chemical reagants). Once separated portions of the gel or medium can be further analyzed to determine the protein constituents of isolated complexes. For example, mass spectrometry and/or liquid chromatography techniques may be employed to identify the protein constituents of a complex.
Proteins identified within a portion can be inferred to be putative members of the same protein complex. Inferences about signaling may also be inferred where one or more proteins are present in a complex in one sample, but are absent from that complex in another sample, for example. However, comparisons between such samples are often difficult to perform with existing technology, and are often performed manually.
It would also be useful to provide a way to interrogate and or compare proteins that are existent in portions of the same sample, as the same protein may be found interacting in different protein complexes of the sample, and/or provide some clue about cell function signaling etc., when such comparisons are made. Again, this is currently very cumbersome to do, often requiring manual review of results from the different portions in an effort to make such comparisons.
Accordingly, there is a need for systems and methods for rapid examination of protein complex data sets to facilitate researchers understanding of functions of and interactions between constituents of the complex datasets.